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static void | addMetaInfoToOptionalColumns (const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta) |
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static std::map< Size, MzTabModificationMetaData > | generateMzTabStringFromModifications (const std::vector< String > &mods) |
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static std::map< Size, MzTabModificationMetaData > | generateMzTabStringFromVariableModifications (const std::vector< String > &mods) |
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static std::map< Size, MzTabModificationMetaData > | generateMzTabStringFromFixedModifications (const std::vector< String > &mods) |
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static MzTab | exportFeatureMapToMzTab (const FeatureMap &feature_map, const String &filename) |
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static MzTab | exportIdentificationsToMzTab (const std::vector< ProteinIdentification > &prot_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &filename, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS") |
| Export peptide and protein identifications to mzTab. More...
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static MzTabModificationList | extractModificationList (const PeptideHit &pep_hit, const std::vector< String > &fixed_mods, const std::vector< String > &localization_mods) |
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static MzTab | exportConsensusMapToMzTab (const ConsensusMap &consensus_map, const String &filename, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const bool export_all_psms=false, const String &title="ConsensusMap export from OpenMS") |
| export linked peptide features aka consensus map More...
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static std::map< String, Size > | mapIDRunIdentifier2IDRunIndex_ (const std::vector< const ProteinIdentification * > &prot_ids) |
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static std::optional< MzTabPSMSectionRow > | PSMSectionRowFromPeptideID_ (PeptideIdentification const &pid, std::vector< ProteinIdentification const * > const &prot_id, std::map< String, size_t > &idrun_2_run_index, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, Size const current_psm_idx, Size const psm_id, MzTabString const &db, MzTabString const &db_version, bool const export_empty_pep_ids, bool const export_all_psms) |
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static MzTabPeptideSectionRow | peptideSectionRowFromConsensusFeature_ (const ConsensusFeature &c, const ConsensusMap &consensus_map, const StringList &ms_runs, const Size n_study_variables, const std::set< String > &consensus_feature_user_value_keys, const std::set< String > &peptide_identifications_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::map< String, size_t > &idrun_2_run_index, const std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, const std::map< std::pair< String, unsigned >, unsigned > &path_label_to_assay, const std::vector< String > &fixed_mods, bool export_subfeatures) |
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static MzTabPeptideSectionRow | peptideSectionRowFromFeature_ (const Feature &c, const std::set< String > &feature_user_value_keys, const std::set< String > &peptide_identifications_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::vector< String > &fixed_mods) |
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static MzTabProteinSectionRow | proteinSectionRowFromProteinHit_ (const ProteinHit &hit, const MzTabString &db, const MzTabString &db_version, const std::set< String > &protein_hit_user_value_keys) |
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static MzTabProteinSectionRow | nextProteinSectionRowFromProteinGroup_ (const ProteinIdentification::ProteinGroup &group, const MzTabString &db, const MzTabString &db_version) |
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static MzTabProteinSectionRow | nextProteinSectionRowFromIndistinguishableGroup_ (const std::vector< ProteinHit > &protein_hits, const ProteinIdentification::ProteinGroup &group, const size_t g, const std::map< Size, std::set< Size >> &ind2prot, const MzTabString &db, const MzTabString &db_version) |
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static void | addMSRunMetaData_ (const std::map< size_t, String > &msrunindex_2_msfilename, MzTabMetaData &meta_data) |
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static void | mapBetweenMSFileNameAndMSRunIndex_ (const std::vector< const ProteinIdentification * > &prot_ids, bool skip_first, std::map< String, size_t > &msfilename_2_msrunindex, std::map< size_t, String > &msrunindex_2_msfilename) |
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static size_t | getQuantStudyVariables_ (const ProteinIdentification &pid) |
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static MzTabParameter | getProteinScoreType_ (const ProteinIdentification &prot_id) |
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static void | getConsensusMapMetaValues_ (const ConsensusMap &consensus_map, std::set< String > &consensus_feature_user_value_keys, std::set< String > &peptide_identification_user_value_keys, std::set< String > &peptide_hit_user_value_keys) |
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static void | getFeatureMapMetaValues_ (const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &peptide_identification_user_value_keys, std::set< String > &peptide_hit_user_value_keys) |
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static void | getIdentificationMetaValues_ (const std::vector< const ProteinIdentification * > &prot_ids, std::vector< const PeptideIdentification * > &peptide_ids_, std::set< String > &protein_hit_user_value_keys, std::set< String > &peptide_id_user_value_keys, std::set< String > &peptide_hit_user_value_keys) |
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static MzTabParameter | getMSRunSpectrumIdentifierType_ (const std::vector< const PeptideIdentification * > &peptide_ids_) |
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static void | mapBetweenRunAndSearchEngines_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::vector< const PeptideIdentification * > &pep_ids, bool skip_first_run, std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, std::map< Size, std::vector< std::vector< std::pair< String, String >>>> &run_to_search_engines_settings, std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings) |
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static std::map< Size, std::set< Size > > | mapGroupsToProteins_ (const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &proteins) |
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static void | addSearchMetaData_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, const std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings, MzTabMetaData &meta_data, bool first_run_inference_only) |
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static void | mapIDRunFileIndex2MSFileIndex_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::map< String, size_t > &msfilename_2_msrunindex, bool skip_first_run, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx) |
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static void | getSearchModifications_ (const std::vector< const ProteinIdentification * > &prot_ids, StringList &var_mods, StringList &fixed_mods) |
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static MzTabString | getModificationIdentifier_ (const ResidueModification &r) |
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static void | checkSequenceUniqueness_ (const std::vector< PeptideIdentification > &curr_pep_ids) |
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Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.